The important effect of soil wetting and drying cycle (WDC) on soil structure, and the consequent effect on pollutant fate is underexplored. We thoroughly investigated the changes in soil structure and in leaching of Alion (indaziflam) and Express (tribenuron methyl), pre and post WDC, from two clayey soils and two loamy soils under different land uses (uncultivated, field crops, and orchards). Soil stability was quantified by an aggregate durability index we recently developed. WDC did not affect the stability of the sandy-loam soils, as expected. However, for the sandy-clay-loam with high CaCO3 content aggregation was observed. For the clayey soils with similar CaCO3, aggregation and disaggregation were obtained, for a soil with relatively low and high SOM, respectively. The stability trends are reflected by the ratio between the contents of inorganic carbon and soil organic matter (SOM), CaCO3/SOM, normalized to the clay content. Aggregation was explained by CaCO3 cementation, while disaggregation was attributed to high clay content and to alterations in SOM conformation post WDC. These opposite trends, obtained for the two clayey soils, were confirmed by analyzing changes in soil packing employing X-ray tomography (micro-CT). Our results clearly demonstrated that soil aggregation and disaggregation, induced by a WDC, suppresses and enhances herbicide mobility, respectively. However, the effect of WDC on herbicide leaching was not noticeable for Alion upon its high adsorption to a clayey soil, indicating that herbicide physical-chemical properties may dominate. Finally, WDC induces micron-scale changes in aggregate structure, which have a notable effect on pollutant mobility and fate in the environment. (C) 2020 Elsevier Ltd. All rights reserved.